Freesurfer

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30132 discussions

R: R: Re: R: Re: analysis on 4-6yrs pat
by crailo＠inwind.it 29 Oct '13

29 Oct '13

Hi Bruce, it seems I have uploaded the dir as well. Thanks for your help! Regards Antonio >----Messaggio originale---- >Da: crailo(a)inwind.it >Data: 25/10/2013 17.02 >A: <fischl(a)nmr.mgh.harvard.edu> >Cc: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: [Freesurfer] R: Re: R: Re: analysis on 4-6yrs pat > >Hi Bruce, >I guess running from scratch is the easiest way. I tried to upload the whole >dir but it seems I cannot have access to it. >Thanks >Regards >Antonio > >>----Messaggio originale---- >>Da: fischl(a)nmr.mgh.harvard.edu >>Data: 25/10/2013 15.33 >>A: "crailo(a)inwind.it"<crailo(a)inwind.it> >>Cc: <freesurfer(a)nmr.mgh.harvard.edu> >>Ogg: Re: [Freesurfer] R: Re: analysis on 4-6yrs pat >> >>Hi Antonio >> >>I need the whole subject directory to diagnose what happened with the FS >>analysis. Or I can try rerunning it from scratch here instead if you >>prefer >>Bruce >>On Fri, 25 Oct 2013, crailo(a)inwind.it wrote: >> >>> Hi Bruce, >>> thanks for the reply. I have uploaded two images, the original one and the >one >>> preprocessed via 3D slicer N3. >>> Thanks >>> Regards >>> Antonio >>> >>>> ----Messaggio originale---- >>>> Da: fischl(a)nmr.mgh.harvard.edu >>>> Data: 25/10/2013 14.07 >>>> A: "crailo(a)inwind.it"<crailo(a)inwind.it> >>>> Cc: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] analysis on 4-6yrs pat >>>> >>>> Hi Antonio >>>> >>>> it's tough to diagnose from one slice. Is the top of the head in general >>>> darker than the bottom? It looks like it, but that might also be lower >>>> myelin content. If you upload the subject we'll take a look. >>>> >>>> cheers >>>> Bruce >>>> On Fri, 25 Oct >>>> 2013, crailo(a)inwind.it wrote: >>>> >>>>> >>>>> Dear Freesurfer experts, >>>>> >>>>> I am trying to run cortical thickness analysis on 4-6 yrs old patients >but >>> I >>>>> have some problem to get nice cortical gray matter. I have tried to run >>>>> several N3 but with no success so I would need to ask whether you could >>> give >>>>> me hints to improve that. Please find attached a screenshot of what I do >>>>> get. >>>>> >>>>> >>>>> Many thanks for any help. >>>>> >>>>> >>>>> Best Wishes >>>>> >>>>> Antonio >>>>> >>>>> >>>>> >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom it >is >>>> addressed. If you believe this e-mail was sent to you in error and the e- >mail >>>> contains patient information, please contact the Partners Compliance >HelpLine >>> at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>>> but does not contain patient information, please contact the sender and >>> properly >>>> dispose of the e-mail. >>>> >>>> >>> >>> >>> >>> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Tracula preprocessing error: cannot find dwi_frames.nii.gz
by Michael Datko 28 Oct '13

28 Oct '13

Hello, I am running into a tracula error very early in the preprocessing steps. I have data that was already somewhat preprocessed (reconstruction, eddy correction and magnetic field inhomogeneity correction) that I'm trying to use as an input. I have turned off those steps in the tracula configuration file. Tracula seems to find these files and starts making a few of the dwi output files in the subject's freesurfer/dmri folder. However, it then says something about not having the correct "frames" and it can't find the file dwi_frames.nii.gz. I'm not sure what this error is referring to. I attempted to run the same subject's data from their raw dicoms instead of the slightly-preprocessed file and also ran into errors. If it makes a difference, the subject had recon-all performed with freesurfer version 5.0 and I am now using version 5.3. Perhaps the subject is missing some necessary recon-all output that is only created with 5.3? Any advice? Thanks, Mike Datko

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Re: [Freesurfer] Freeview
by Lindsay Squeglia 28 Oct '13

28 Oct '13

It was definitely from freeview. These are the notes I wrote for creating figures previously, and I didn't have a problem: **Type freeview in command line in file where Freesurfer fsaverage brain is, will open file, go to File--> Load Surface -->fsaverage-->surf. Choose lh.pial; then do again for rh.pial for the pial surfaces. Go to View--> Show Control Panel, click on 1x1 view (white box at top of control panel), click on face (says 3D ALT3, at top of control panel, next to MRIs), Change Edge thickness=0 (to remove yellow lines), Change curvature=off (to make brain gray), (Must do all of this for L and R hemis separately). Label: load brain region (Label--> Load from file) you want from your Labels_from_parc file. Then you can change color accordingly. On Mon, Oct 28, 2013 at 11:58 AM, Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu>wrote: > Was that from freeview or tksurfer? > > On 10/28/2013 02:06 PM, Lindsay Squeglia wrote: > > Hi Ruopeng, > > Thanks for your response! I used to do it all the time in the previous > versions of FreeSurfer (see attached). I am not sure why the new version is > different. > > Thanks! > Lindsay > > > > > On Mon, Oct 28, 2013 at 11:01 AM, Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu > > wrote: > >> Hi Lindsay, >> >> I think there was no such option to display multiple surface labels at >> once even in the old version. However, we will add it in the future. >> >> Best, >> Ruopeng >> >> >> On 10/28/2013 01:48 PM, Lindsay Squeglia wrote: >> >> Hi all, >> >> I recently updated to FreeSurfer version 5.3.0, and I am now having >> problems with freeview that I didn't have on the older versions. When I go >> to "Surfaces" and "Load Labels", it only shows one label at a time. >> Previously, I could add several labels and all would appear on the Figure. >> Does anyone know a fix for this? >> >> Thanks! >> Lindsay >> >> >> >> >> _______________________________________________ >> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > > > -- > Lindsay M. Squeglia, Ph.D. > Postdoctoral Fellow > University of California San Diego > office phone: 858-822-2306 > email: lsquegli(a)ucsd.edu > > > -- Lindsay M. Squeglia, Ph.D. Postdoctoral Fellow University of California San Diego office phone: 858-822-2306 email: lsquegli(a)ucsd.edu

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Re: [Freesurfer] sim ocn clusters mean effect size
by Kayle Sawyer 28 Oct '13

28 Oct '13

Hi all, I would like to calculate the 95% confidence interval of the slope for a thickness cluster (vs age in years) produced by mri_glmfit-sim. I have obtained values for my clusters from gamma.mgh and gammavar.mgh using these two commands: mri_segstats --i gamma.mgh --seg mc-z.th1.3.neg.sig.ocn.mgh --excludeid 0 --sum mc-z.th1.3.neg.sig.ocn.gamma.segstats mri_segstats --i gammavar.mgh --seg mc-z.th1.3.neg.sig.ocn.mgh --excludeid 0 --sum mc-z.th1.3.neg.sig.ocn.gammavar.segstats Next, (for each cluster, within each segstats summary file) I would take the “mean” from gamma, and the “mean” from gammavar, and calculate the positive 95% CI thus: gamma + 1.96*sqrt(gammavar) gamma - 1.96*sqrt(gammavar) Would these two values would give me the 95% confidence interval for the effect of age on that cluster, in mm/year? Thanks, -Kayle

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Re: [Freesurfer] Freeview
by Ruopeng Wang 28 Oct '13

28 Oct '13

Was that from freeview or tksurfer? On 10/28/2013 02:06 PM, Lindsay Squeglia wrote: > Hi Ruopeng, > > Thanks for your response! I used to do it all the time in the previous > versions of FreeSurfer (see attached). I am not sure why the new > version is different. > > Thanks! > Lindsay > > > > > On Mon, Oct 28, 2013 at 11:01 AM, Ruopeng Wang > <rpwang(a)nmr.mgh.harvard.edu <mailto:rpwang@nmr.mgh.harvard.edu>> wrote: > > Hi Lindsay, > > I think there was no such option to display multiple surface > labels at once even in the old version. However, we will add it in > the future. > > Best, > Ruopeng > > > On 10/28/2013 01:48 PM, Lindsay Squeglia wrote: >> Hi all, >> >> I recently updated to FreeSurfer version 5.3.0, and I am now >> having problems with freeview that I didn't have on the older >> versions. When I go to "Surfaces" and "Load Labels", it only >> shows one label at a time. Previously, I could add several labels >> and all would appear on the Figure. Does anyone know a fix for this? >> >> Thanks! >> Lindsay >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > -- > Lindsay M. Squeglia, Ph.D. > Postdoctoral Fellow > University of California San Diego > office phone: 858-822-2306 > email: lsquegli(a)ucsd.edu <mailto:lsquegli@ucsd.edu>

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Issue with 5.3.0 nu_correction?
by Natalie Garcia 28 Oct '13

28 Oct '13

Hi all, I've tried running auto-recon with version 5.3.0 (on Mac OSX v10.8.2) and the processing stream seems to fail at the intensity correction point. Not sure if it helps, but when I look at the output from the PBS script, I see "nu_correct: Command not found." Any suggestions on what I might be able to do to fix this? Any help would be greatly appreciated. Natalie -- Natalie V. Garcia Graduate Student, Cognitive Psychology Psychology Department The Pennsylvania State University 423 Moore Building nvg109(a)psu.edu

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Freeview
by Lindsay Squeglia 28 Oct '13

28 Oct '13

Hi all, I recently updated to FreeSurfer version 5.3.0, and I am now having problems with freeview that I didn't have on the older versions. When I go to "Surfaces" and "Load Labels", it only shows one label at a time. Previously, I could add several labels and all would appear on the Figure. Does anyone know a fix for this? Thanks! Lindsay

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Problem generating volume stats with hippocampal segmentation script
by Erin Walsh 28 Oct '13

28 Oct '13

Hi, I'm experiencing a problem when running the automated hippocampal subfield segmentation script. Unfortunately, I have been unable to determine the cause of the error. After reconstructing all participant data with the -hippo-subfields flag, I ran the "kvlQuantifyHippocampalSubfieldSegmentations.sh" script. The script seems to be working fine, generating subfield values for all participants until the very end when it attempts to generate the stat tables (I think). At this point, I receive the following error: /Applications/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: volumeStats_left.txt: Permission denied failed to do kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt I've copied some output and the error message below, including the last participant in our folder it runs through before attempting to generate volume stats. Thanks for any help you can offer! Best Erin -- Erin Walsh, Ph.D. Postdoctoral Research Associate University of Wisconsin-Madison Department of Psychiatry: Abercrombie Lab<http://www.psychiatry.wisc.edu/abercrombie/> 6001 Research Park Blvd. Madison, WI 53719 edubwalsh(a)gmail.com Relevant information: FREESURFER_HOME: /Applications/freesurfer Current working dir ran command: /Applications/freesurfer/subjects/CORTMR/recon Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.4.0 x86_64 Command line ran: kvlQuantifyHippocampalSubfieldSegmentations.sh Output/Error (after seemingly generating hippocampal subfield values for all participants): ... cd 228/ Quantifying subject 228/ left Doing left side cd mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt cd .. Quantifying subject 228/ right Doing right side cd mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2_3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4_DG.mgz posterior_right_hippocampal_fissure.mgz > volumeStats_right.txt cd .. cd .. cd fsaverage/ Quantifying subject fsaverage/ left Doing left side cd mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt /Applications/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: volumeStats_left.txt: Permission denied failed to do kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt

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CVS registration questions
by raij＠nmr.mgh.harvard.edu 28 Oct '13

28 Oct '13

Hi Lilla et al, I am preparing to CVS register 30+ subjects to improve FSL probabilistic tractography alignment across subjects. First, thanks for a really cool tool! Then, I have some questions: 1. mri_cvs_register step1 is spherical registration. However, I have already run FS5.3 recon-all -all for all subjects, which includes spherical registration. Are the recon-all and mri_cvs_register spherical registrations identical? If so, will mri_cvs_register be able to use the previously computed spherical registration (with flags --step2 --step3), or will it need to compute a new spherical registration? Will mri_cvs_register overwrite any of my earlier recon-all results? 2. What are the pros and cons for using one of the following as templates, and which one would you recommend: -Randomly selected individual subject -CVS35 -CVS35_inMNI152 3. When using MNI152_1mm as template, I guess this is a 1 mm resolution image (as $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/T1.mgz seems to be in 1 mm resolution)? Technically, is this the cvs_avg35 image that has been CVS-registered with the MNI152_1mm image? Or is this a FLIRT-type 3D registration from cvs_avg35 to MNI152_1mm without surface information (I guess extracting the surface from MNI152 would be difficult)? 4. I run into the following error in FS stable 5.3 (source /usr/local/freesurfer/nmr-stable53-env): mri_cvs_check --mov $SUBJECT Using the CVS template as registration target. The following files are missing: /usr/local/freesurfer/stable5_3_0/bin/mri_cvs_register.settings.txt You need to find these files or run reconall on the data in order to run mri_cvs_register. Is this file required, or is this a bogus error? 5. Are there parallel processing versions that could be run on the cluster? Thanks! Tommi --- Tommi Raij, MD, PhD TM Core Director MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz doesnot have mri_strip_skull codes
by Rujing Zha 28 Oct '13

28 Oct '13

Dear FreeSurfer Users, I downloaded FreeSurfer latest version in this website:ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurf…. I want to strip 3d structure skull by mri_strp_skull,but this package does not have this codes.Why? What else can I do? Thanks! Any reply and advice will be appreciated! Best. 2013-10-28 Rujing Zha

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